Designing nanoscale systems often requires repeated arrangements of atoms or molecular fragments—think helices, nanotubes, or crystal-like lattices. Yet, replicating and aligning these geometries manually can quickly become tedious and error-prone. That’s where SAMSON’s Pattern Editors come in: intuitive tools that help you create linear, circular, and curved molecular arrays efficiently and interactively.
Whether you’re modeling DNA origami, chaining functional groups, or building nanomaterials, SAMSON offers a visual and flexible way to go from a single monomer to hundreds or thousands of precise, spatially-organized instances.
Why this matters
Biomolecular and nanotechnological models often depend on the controlled repetition of molecular motifs. Patterns such as stacked rings, coiled helices, or 2D sheets emerge naturally in proteins, carbon nanostructures, and synthetic materials—but aligning each instance by hand isn’t practical, especially when working with large assemblies.
SAMSON’s Pattern Editors (linear, curved, and circular) automate this with live on-screen widgets, precise controls, and snapping features to make model building faster and more reproducible.
Three editors, many possibilities
Use the following editors depending on your structure’s symmetry or motif:
- Linear Pattern Editor – replicate structures along a straight path ✳️
- Circular Pattern Editor – arrange copies around a central axis 🔄
- Curved Pattern Editor – arrange replicas along a user-defined curve 🌀
How to use pattern editors effectively
- Select what to repeat: this could be a single ring, a functional group, or a more complex fragment.
- Activate an editor: press L, W, or Q to open linear, circular, or curved pattern editors, respectively.
- Adjust geometry in the viewport:
- Use drag handles to interactively move and rotate structures.
- Click the center of widgets to enter exact angles or translations.
- Scroll the mouse wheel over the widget to change copy count.
- Use snapping to ensure proper alignment or symmetry, especially useful for bonding or interface design.
- Click Accept to bake the pattern into your document.
Example: stacking a nanoring into a nanotube
A frequent task in nanotechnology is creating stacked rings for nanotubes. With SAMSON, you can:
- Create a base ring fragment.
- Use the Circular Pattern Editor to form a closed loop of fragments.
- Align and merge overlapping atoms to finalize the ring.
- Switch to the Linear Pattern Editor to stack rings vertically to form a tube.
- Rotate and translate with control to match bonds and symmetry.
This pattern-building workflow enables you to diagram complex architectures without extensive manual placement.
Advanced options
In SAMSON preferences, you can further streamline your modeling by choosing to:
- Automatically merge overlapping atoms
- Adjust terminal hydrogens
- Decide whether new copies are grouped or fused into one structure
These options provide more control over the specific needs of your molecular design, especially when combining fragments from varied sources.
Visual feedback while designing
All pattern editors include on-screen manipulators so you can see each replicated copy before confirming. Whether spacing a linear chain, building a wheel of molecules, or curling structures onto a surface, what you see is what you get. This reduces trial and error and helps you build intuition for spatial arrangements.
To explore more examples and features, see the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.